LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-605-g5eb61491f0-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University

# Initiation -------------------------------------
units           metal
dimension       3
boundary        p p p
atom_style      atomic


# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region          whole block 0 1 0 1 0 1
create_box      2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
  1 by 1 by 1 MPI processor grid
create_atoms    1 region whole
Created 4 atoms
  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
  create_atoms CPU = 0.000 seconds

replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
  1 by 1 by 1 MPI processor grid
  2304 atoms
  replicate CPU = 0.000 seconds

region      puck block INF INF INF 2 INF INF
set         region puck type 2
Setting atom values ...
  360 settings made for type

# Force Fields -----------------------------------
pair_style      meam
pair_coeff      * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08

# Settings ---------------------------------------
timestep        0.002
thermo          100

# Computations -----------------------------------
compute         voroN all voronoi/atom neighbors yes

run             0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 7 18 7
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair meam, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (2) pair meam, perpetual, half/full from (1)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -9674.3728      0             -9674.3728     -212400.94    
Loop time of 7.92e-07 on 1 procs for 0 steps with 2304 atoms

126.3% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 7.92e-07   |            |       |100.00

Nlocal:           2304 ave        2304 max        2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           4735 ave        4735 max        4735 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          99072 ave       99072 max       99072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       198144 ave      198144 max      198144 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe

# Execution --------------------------------------

velocity    all create 2400 908124 loop geom
fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump           dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym

run 1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix neighbor/swap command: doi:10.1016/j.commatsci.2022.111929

@Article{Tavenner2023111929,
 author = {Jacob P. Tavenner and Mikhail I. Mendelev and John W. Lawson},
 title = {Molecular dynamics based kinetic Monte Carlo simulation for accelerated diffusion},
 journal = {Computational Materials Science},
 year = {2023},
 volume = {218},
 pages = {111929}
 url = {https://dx.doi.org/10.1016/j.commatsci.2022.111929}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
         0   2400          -187517.52     -187464.47     -188202.62     -186885.48      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
       100   1665.6154      14281.316      14426.547      14555.867      13861.534      21.637238      57.719793      21.637281      27022.733     -9594.4303      24             24           
       200   1603.3309     -7325.7341     -8878.1524     -5333.0485     -7766.0015      21.710246      58.122827      21.725933      27415.106     -9577.4545      48             48           
       300   1603.2974      207.19165      1983.4565     -1841.9518      480.07024      21.678227      58.079126      21.674033      27288.745     -9577.6391      72             69           
       400   1600.1515      810.95054      1087.969       802.04946      542.83316      21.683731      58.045848      21.678505      27285.662     -9576.6508      96             92           
       500   1629.8313     -2808.1005     -3197.9357      310.89931     -5537.265       21.683924      58.090375      21.697076      27330.229     -9585.5435      120            113          
       600   1598.8232     -67.845623     -1573.0718     -1526.7607      2896.2957      21.70213       58.12191       21.653853      27313.504     -9576.4147      144            137          
       700   1607.2185      154.66718     -1777.2469      2566.4705     -325.22208      21.712408      57.971553      21.678708      27287.033     -9579.1772      168            158          
       800   1582.559      -891.23631     -632.46037     -636.88203     -1404.3665      21.671936      58.127004      21.678224      27308.594     -9571.6663      192            180          
       900   1586.7172     -617.17083     -2495.5378     -2302.8766      2946.9018      21.658489      58.181921      21.668968      27305.771     -9572.9641      216            204          
      1000   1607.563      -389.8113       810.4908       298.84287     -2278.7676      21.624573      58.076745      21.724272      27283.183     -9579.5034      240            227          
Loop time of 31.1311 on 1 procs for 1000 steps with 2304 atoms

Performance: 5.551 ns/day, 4.324 hours/ns, 32.122 timesteps/s, 74.010 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.859     | 27.859     | 27.859     |   0.0 | 89.49
Neigh   | 0.22271    | 0.22271    | 0.22271    |   0.0 |  0.72
Comm    | 0.012597   | 0.012597   | 0.012597   |   0.0 |  0.04
Output  | 0.00031219 | 0.00031219 | 0.00031219 |   0.0 |  0.00
Modify  | 3.0301     | 3.0301     | 3.0301     |   0.0 |  9.73
Other   |            | 0.006178   |            |       |  0.02

Nlocal:           2304 ave        2304 max        2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           4748 ave        4748 max        4748 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         130301 ave      130301 max      130301 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       260602 ave      260602 max      260602 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 260602
Ave neighs/atom = 113.10851
Neighbor list builds = 62
Dangerous builds = 0

#write_data     pulse_end.data
Total wall time: 0:00:31
